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Started by upstream project "BIOFORMATS-test-repo" build number 228 originally caused by: Started by upstream project "Trigger" build number 253 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins9675104194331757582.sh + '[' zip = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35729_merge_ci -v /uod/idr/repos/curated/zip:/data -v /uod/idr-scratch/merge-ci/curated/zip:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12 Buildfile: /bio-formats-build/bioformats/components/test-suite/build.xml [echo] isSnapshot = true init-title: [echo] ----------=========== bio-formats-testing-framework ===========---------- init-timestamp: init: copy-resources: compile: [resolver:resolve] Resolving artifacts compile-tests: [resolver:resolve] Resolving artifacts [javac] Compiling 1 source file to /bio-formats-build/bioformats/components/test-suite/test [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] 1 warning test-automated: [testng] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 01:30:40,870 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:30:40,872 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 01:30:40,872 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:30:40,873 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:30:40,874 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:30:40,874 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:30:40,875 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:30:40,875 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:30:40,875 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:30:40,876 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:30:40,876 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:30:40,876 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:30:41,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:30:41,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:30:41,078 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:30:41,078 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:30:41,085 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:30:41,085 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:30:41,085 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:30:41,085 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:30:41,085 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 01:30:41,086 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 01:30:41,086 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 211 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-19 01:30:41,096] [main] java.version = 11.0.16 [testng] 01:30:41,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:30:41,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:30:41,143 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-19_01-30-41.log] [testng] 01:30:41,145 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-19 01:30:41,147] [main] testng.directory = /data [testng] [2024-10-19 01:30:41,147] [main] testng.configDirectory = /config [testng] [2024-10-19 01:30:41,157] [main] testng.multiplier = 1.0 [testng] [2024-10-19 01:30:41,158] [main] testng.in-memory = false [testng] [2024-10-19 01:30:41,159] [main] testng.allow-missing = false [testng] [2024-10-19 01:30:41,159] [main] user.language = en [testng] [2024-10-19 01:30:41,159] [main] user.country = ${user.country} [testng] [2024-10-19 01:30:41,159] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-19 01:30:41,719] [main] ---------------------------------------- [testng] [2024-10-19 01:30:41,719] [main] Total files: 22 [testng] [2024-10-19 01:30:41,720] [main] Scan time: 0.56 s (25 ms/file) [testng] [2024-10-19 01:30:41,720] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-19 01:32:27,136] [pool-1-thread-1] Initializing /data/imagej/blood-brain-barrier.zip: [testng] 01:32:27,137 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:32:27,137 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:27,139 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-19_01-32-27.log] [testng] 01:32:27,139 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62ae4573 - End of configuration. [testng] [2024-10-19 01:32:36,819] [pool-1-thread-12] Initializing /data/imagej/confocal-series.zip: [testng] 01:32:36,819 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:32:36,819 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:36,820 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-19_01-32-36.log] [testng] 01:32:36,820 |-INFO in ch.qos.logback.core.sift.SiftProcessor@474d4e42 - End of configuration. [testng] [2024-10-19 01:32:43,942] [pool-1-thread-11] Initializing /data/imagej/m51.zip: [testng] 01:32:43,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:32:43,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:43,943 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-19_01-32-43.log] [testng] 01:32:43,944 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78e15646 - End of configuration. [testng] [2024-10-19 01:32:45,723] [pool-1-thread-10] Initializing /data/imagej/xrays.zip: [testng] 01:32:45,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:32:45,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:45,724 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-19_01-32-45.log] [testng] 01:32:45,725 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f93751 - End of configuration. [testng] [2024-10-19 01:32:47,331] [pool-1-thread-9] Initializing /data/imagej/se3.zip: [testng] 01:32:47,331 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:32:47,331 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:47,332 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-19_01-32-47.log] [testng] 01:32:47,332 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36e541a1 - End of configuration. [testng] [2024-10-19 01:32:55,293] [pool-1-thread-8] Initializing /data/imagej/mri-stack.zip: [testng] 01:32:55,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:32:55,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:55,294 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-19_01-32-55.log] [testng] 01:32:55,294 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7667eb9e - End of configuration. [testng] [2024-10-19 01:32:57,509] [pool-1-thread-7] Initializing /data/imagej/RatBrain.zip: [testng] 01:32:57,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:32:57,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:57,510 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-19_01-32-57.log] [testng] 01:32:57,511 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3aace575 - End of configuration. [testng] [2024-10-19 01:33:00,014] [pool-1-thread-6] Initializing /data/imagej/scala-media.zip: [testng] 01:33:00,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:33:00,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:00,014 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-19_01-33-00.log] [testng] 01:33:00,015 |-INFO in ch.qos.logback.core.sift.SiftProcessor@178a1e09 - End of configuration. [testng] [2024-10-19 01:33:03,081] [pool-1-thread-5] Initializing /data/imagej/3D_Chromosome.zip: [testng] 01:33:03,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:33:03,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:03,081 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-19_01-33-03.log] [testng] 01:33:03,082 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1dfa18 - End of configuration. [testng] [2024-10-19 01:33:07,525] [pool-1-thread-4] Initializing /data/imagej/gel-electrophoresis.zip: [testng] 01:33:07,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:33:07,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:07,526 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-19_01-33-07.log] [testng] 01:33:07,527 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38f94840 - End of configuration. [testng] [2024-10-19 01:33:12,400] [pool-1-thread-3] Initializing /data/imagej/flybrain.zip: [testng] 01:33:12,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:33:12,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:12,401 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-19_01-33-12.log] [testng] 01:33:12,402 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17be8144 - End of configuration. [testng] [2024-10-19 01:33:20,816] [pool-1-thread-2] Initializing /data/imagej/hela-cells.zip: [testng] 01:33:20,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:33:20,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:20,817 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-19_01-33-20.log] [testng] 01:33:20,817 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60cb4eda - End of configuration. [testng] [2024-10-19 01:33:47,073] [pool-1-thread-11] Initializing /data/samples/bat-cochlea-volume.zip: [testng] [2024-10-19 01:33:50,862] [pool-1-thread-10] Initializing /data/imagej/fat-cells.zip: [testng] [2024-10-19 01:33:55,140] [pool-1-thread-6] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] [2024-10-19 01:33:59,227] [pool-1-thread-8] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] [2024-10-19 01:34:02,144] [pool-1-thread-7] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] [2024-10-19 01:34:10,570] [pool-1-thread-5] Initializing /data/imagej/FluorescentCells.zip: [testng] [2024-10-19 01:34:28,965] [pool-1-thread-2] Initializing /data/imagej/confocal-stack.zip: [testng] [2024-10-19 01:34:50,350] [pool-1-thread-5] Initializing /data/imagej/watershed-animation.zip: [testng] [2024-10-19 01:34:52,360] [pool-1-thread-8] Initializing /data/samples/sdub.zip: [testng] [2024-10-19 01:34:53,517] [pool-1-thread-4] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1166, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 8 minutes 29 seconds Finished: SUCCESS